RetrogeneDB ID: retro_hvul_39

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:147398739..147399195(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_23439
• Aliases: None
• Description: None

Sequence

>retro_hvul_39
CCGCAGTGGCTGCGCCCGCTGCTGTCCGCGCGCTTCTTCGCGCAATGCAAGACGCACTCCGAGTCGCACCGGAGCGGCGA
GTGCAACATGTTCTGCCTCGACTGCGCCGCCGGGGCCGCCGCCGGCGCGGCGGCGCTGTGCTCGCTGTGCCTCGCGCACG
GGCACCGGGGGCACCACACCATCCAGATCCGCCGCTCCTCCTACCACGACGTCATCCGGGTGTCAGACATCCAGCGCTTC
ATGGACATCGCCGGCGTGCAGACCTACGTCATCAACAGCGCCCGCGTCGTCTTCCTCAACGAGCGGCCCCAGCAGAAGCA
GCCCGGCAAGGGCGGCGGCGGCGGCGGCGCCGGGAGCGCCAACCTCTGCGAGGTCTGCAGCCGCAGCCTCCTCGACAACT
TCCGCTTCTGCTCCCTCGGCTGCAAGGTGGCCGGCTGCTCCTCCGACGGGGGCGGC

Alignment

ORF - retro_hvul_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.61 %
• Parental protein coverage: 68.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGWLEALLGTRFFLACAAHPGSPRN-ECNMFCIDCR----ATPAAFCYYCRSHRHAAHRVIQIRRSSYHD
          P.WL..LL..RFF..C..H..S.R..ECNMFC.DC.....A..AA.C..C..H.H..H..IQIRRSSYHD
Retrocopy PQWLRPLLSARFFAQCKTHSESHRSGECNMFCLDCAAGAAAGAAALCSLCLAHGHRGHHTIQIRRSSYHD

Parental  VVRVTEVEDVLDIAGVQTYVINSARVLFLNERPQPRGAGAAAGKAAASPYN-CEICGRALLDPFRFCSLG
          V.RV.......DIAGVQTYVINSARV.FLNERPQ....G...........N.CE.C.R.LLD.FRFCSLG
Retrocopy VIRVSDIQRFMDIAGVQTYVINSARVVFLNERPQQKQPGKXXXXXXXGSANLCEVCSRSLLDNFRFCSLG

Parental  CKLVDTKTHGHG
          CK.......G.G
Retrocopy CKVAGCSSDGGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_39 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_23439	1 retrocopy	retro_hvul_39 ,
Triticum aestivum	Traes_7DS_620E0D488	1 retrocopy	retro_taes_8,